Improving AlphaFold2- and AlphaFold3-Based Protein Complex Structure Prediction With MULTICOM4 in CASP16.

ABSTRACT: With AlphaFold achieving high-accuracy tertiary structure prediction for most single-chain proteins (monomers), the next major challenge in protein structure prediction is to accurately model multichain protein complexes (multimers). We developed MULTICOM4, the latest version of the MULTICOM system, to improve protein complex structure prediction by integrating transformer-based AlphaFold2, diffusion model-based AlphaFold3, and our in-house techniques. These include protein complex stoichiometry prediction, diverse multiple sequence alignment (MSA) generation leveraging both sequence and structure comparison, modeling exception handling, and deep learning-based protein model quality assessment. MULTICOM4 was blindly evaluated in the 16th Critical Assessment of Techniques for Protein Struct

SUBMITTER: Liu J 

PROVIDER: S-EPMC12354153 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature